OpenRaiser/Intern-Atlas huggingface dataset:
Positive-Unlabelled Learning for identifying new candidate Dietary Restriction-related genes among Ageing-related genes
Venue: arXiv cs.LG 2025
Year: 2025

Dietary Restriction (DR) is one of the most popular anti-ageing interventions; recently, Machine Learning (ML) has been explored to identify potential DR-related genes among ageing-related genes, aiming to minimize costly wet lab experiments needed to expand our knowledge on DR. However, to train a model from positive (DR-related) and negative (non-DR-related) examples, the existing ML approach naively labels genes without known DR relation as negative examples, assuming that lack of DR-related annotation for a gene represents evidence of absence of DR-relatedness, rather than absence of evidence. This hinders the reliability of the negative examples (non-DR-related genes) and the method's ability to identify novel DR-related genes. This work introduces a novel gene prioritisation method based on the two-step Positive-Unlabelled (PU) Learning paradigm: using a similarity-based, KNN-inspired approach, our method first selects reliable negative examples among the genes without known DR associations. Then, these reliable negatives and all known positives are used to train a classifier that effectively differentiates DR-related and non-DR-related genes, which is finally employed to generate a more reliable ranking of promising genes for novel DR-relatedness. Our method significantly outperforms (p<0.05) the existing state-of-the-art approach in three predictive accuracy metrics with up to 40% lower computational cost in the best case, and we identify 4 new promising DR-related genes (PRKAB1, PRKAB2, IRS2, PRKAG1), all with evidence from the existing literature supporting their potential DR-related role.
Provably Robust Pre-Trained Ensembles for Biomarker-Based Cancer Classification
Venue: arXiv cs.LG 2025
Year: 2025

Certain cancer types, notably pancreatic cancer, are difficult to detect at an early stage, motivating robust biomarker-based screening. Liquid biopsies enable non-invasive monitoring of circulating biomarkers, but typical machine learning pipelines for high-dimensional tabular data (e.g., random forests, SVMs) rely on expensive hyperparameter tuning and can be brittle under class imbalance. We leverage a meta-trained Hyperfast model for classifying cancer, accomplishing the highest AUC of 0.9929 and simultaneously achieving robustness especially on highly imbalanced datasets compared to other ML algorithms in several binary classification tasks (e.g. breast invasive carcinoma; BRCA vs. non-BRCA). We also propose a novel ensemble model combining pre-trained Hyperfast model, XGBoost, and LightGBM for multi-class classification tasks, achieving an incremental increase in accuracy (0.9464) while merely using 500 PCA features; distinguishable from previous studies where they used more than 2,000 features for similar results. Crucially, we demonstrate robustness under class imbalance: empirically via balanced accuracy and minority-class recall across cancer-vs.-noncancer and cancer-vs.-rest settings, and theoretically by showing (i) a prototype-form final layer for Hyperfast that yields prior-insensitive decisions under bounded bias, and (ii) minority-error reductions for majority vote under mild error diversity. Together, these results indicate that pre-trained tabular models and simple ensembling can deliver state-of-the-art accuracy and improved minority-class performance with far fewer features and no additional tuning.
VANE-Bench: Video Anomaly Evaluation Benchmark for Conversational LMMs
Venue: arXiv cs.CV 2025
Year: 2025

The recent developments in Large Multi-modal Video Models (Video-LMMs) have significantly enhanced our ability to interpret and analyze video data. Despite their impressive capabilities, current Video-LMMs have not been evaluated for anomaly detection tasks, which is critical to their deployment in practical scenarios e.g., towards identifying deepfakes, manipulated video content, traffic accidents and crimes. In this paper, we introduce VANE-Bench, a benchmark designed to assess the proficiency of Video-LMMs in detecting and localizing anomalies and inconsistencies in videos. Our dataset comprises an array of videos synthetically generated using existing state-of-the-art text-to-video generation models, encompassing a variety of subtle anomalies and inconsistencies grouped into five categories: unnatural transformations, unnatural appearance, pass-through, disappearance and sudden appearance. Additionally, our benchmark features real-world samples from existing anomaly detection datasets, focusing on crime-related irregularities, atypical pedestrian behavior, and unusual events. The task is structured as a visual question-answering challenge to gauge the models' ability to accurately detect and localize the anomalies within the videos. We evaluate nine existing Video-LMMs, both open and closed sources, on this benchmarking task and find that most of the models encounter difficulties in effectively identifying the subtle anomalies. In conclusion, our research offers significant insights into the current capabilities of Video-LMMs in the realm of anomaly detection, highlighting the importance of our work in evaluating and improving these models for real-world applications. Our code and data is available at https://hananshafi.github.io/vane-benchmark/
Unlocking Large Language Model's Planning Capabilities with Maximum Diversity Fine-tuning
Venue: arXiv cs.AI 2025
Year: 2025

Large language models (LLMs) have demonstrated impressive task-solving capabilities through prompting techniques and system designs, including solving planning tasks (e.g., math proofs, basic travel planning) when sufficient data is available online and used during pre-training. However, for planning tasks with limited prior data (e.g., blocks world, advanced travel planning), the performance of LLMs, including proprietary models like GPT and Gemini, is poor. This paper investigates the impact of fine-tuning on the planning capabilities of LLMs, revealing that LLMs can achieve strong performance in planning through substantial (tens of thousands of specific examples) fine-tuning. Yet, this process incurs high economic, time, and computational costs for each planning problem variation. To address this, we propose Clustering-Based Maximum Diversity Sampling (CMDS), which selects diverse and representative data to enhance sample efficiency and the model's generalization capability. Extensive evaluations demonstrate that CMDS-l, a baseline method combining CMDS with language embeddings, outperforms random sampling. Furthermore, we introduce a novel algorithm, CMDS-g, which encodes planning task instances with their graph representations into the embedding space. Empirical results show that CMDS-g consistently outperforms baseline methods across various scales and multiple benchmark domains.
Task Facet Learning: A Structured Approach to Prompt Optimization
Venue: arXiv cs.AI 2025
Year: 2025

Given a task in the form of a basic description and its training examples, prompt optimization is the problem of synthesizing the given information into a text prompt for a large language model. Humans solve this problem by also considering the different facets that define a task (e.g., counter-examples, explanations, analogies) and including them in the prompt. However, it is unclear whether existing algorithmic approaches, based on iteratively editing a given prompt or automatically selecting a few in-context examples, can cover the multiple facets required to solve a complex task. In this work, we view prompt optimization as that of learning multiple facets of a task from a set of training examples. We exploit structure in the prompt optimization problem and break down a prompt into loosely coupled semantic sections. The proposed algorithm, UniPrompt, (1) clusters the input space and uses clustered batches so that each batch likely corresponds to a different facet of the task, and (2) utilizes a feedback mechanism to propose adding, editing or deleting a section, which in turn is aggregated over a batch to capture generalizable facets. Empirical evaluation on multiple datasets and a real-world task shows that prompts generated using \shortname{} obtain higher accuracy than human-tuned prompts and those from state-of-the-art methods. In particular, our algorithm can generate long, complex prompts that existing methods are unable to generate. Code for UniPrompt is available at https://aka.ms/uniprompt.
Graph Neural Backdoor: Fundamentals, Methodologies, Applications, and Future Directions
Venue: arXiv cs.LG 2025
Year: 2025

Graph Neural Networks (GNNs) have significantly advanced various downstream graph-relevant tasks, encompassing recommender systems, molecular structure prediction, social media analysis, etc. Despite the boosts of GNN, recent research has empirically demonstrated its potential vulnerability to backdoor attacks, wherein adversaries employ triggers to poison input samples, inducing GNN to adversary-premeditated malicious outputs. This is typically due to the controlled training process, or the deployment of untrusted models, such as delegating model training to third-party service, leveraging external training sets, and employing pre-trained models from online sources. Although there's an ongoing increase in research on GNN backdoors, comprehensive investigation into this field is lacking. To bridge this gap, we propose the first survey dedicated to GNN backdoors. We begin by outlining the fundamental definition of GNN, followed by the detailed summarization and categorization of current GNN backdoor attacks and defenses based on their technical characteristics and application scenarios. Subsequently, the analysis of the applicability and use cases of GNN backdoors is undertaken. Finally, the exploration of potential research directions of GNN backdoors is presented. This survey aims to explore the principles of graph backdoors, provide insights to defenders, and promote future security research.
RGBlimp-Q: Robotic Gliding Blimp With Moving Mass Control Based on a Bird-Inspired Continuum Arm
Venue: arXiv cs.RO 2025
Year: 2025

Robotic blimps, as lighter-than-air aerial platforms, offer extended operational duration and enhanced safety in human-robot interactions due to their buoyant lift. However, achieving robust flight performance under environmental airflow disturbances remains a critical challenge, thereby limiting their broader deployment. Inspired by avian flight mechanics, particularly the ability of birds to perch and stabilize in turbulent wind conditions, this article introduces RGBlimp-Q -- a robotic gliding blimp equipped with a bird-inspired continuum arm featuring a novel moving mass actuation mechanism. This continuum arm enables flexible attitude regulation through internal mass redistribution, significantly enhancing the system's resilience to external disturbances. In addition, it facilitates aerial manipulation by employing end-effector claws that interact with the environment in a manner analogous to avian perching behavior. This article presents the design, modeling, and prototyping of RGBlimp-Q, supported by comprehensive experimental evaluation and comparative analysis. To the best of the authors' knowledge, this represents the first interdisciplinary integration of continuum mechanisms into a lighter-than-air robotic platform, where the continuum arm simultaneously functions as both an actuation and manipulation module. This design establishes a novel paradigm for robotic blimps, expanding their applicability to complex and dynamic environments.
Balancing Rigor and Utility: Mitigating Cognitive Biases in Large Language Models for Multiple-Choice Questions
Venue: arXiv cs.CL 2025
Year: 2025

This paper examines the role of cognitive biases in the decision-making processes of large language models (LLMs), challenging the conventional goal of eliminating all biases. When properly balanced, we show that certain cognitive biases can enhance decision-making efficiency through rational deviations and heuristic shortcuts. By introducing heuristic moderation and an abstention option, which allows LLMs to withhold responses when uncertain, we reduce error rates, improve decision accuracy, and optimize decision rates. Using the Balance Rigor and Utility (BRU) dataset, developed through expert collaboration, our findings demonstrate that targeted inspection of cognitive biases aligns LLM decisions more closely with human reasoning, enhancing reliability and suggesting strategies for future improvements. This approach offers a novel way to leverage cognitive biases to improve the practical utility of LLMs across various applications.
From Intentions to Techniques: A Comprehensive Taxonomy and Challenges in Text Watermarking for Large Language Models
Venue: arXiv cs.CL 2025
Year: 2025

With the rapid growth of Large Language Models (LLMs), safeguarding textual content against unauthorized use is crucial. Watermarking offers a vital solution, protecting both - LLM-generated and plain text sources. This paper presents a unified overview of different perspectives behind designing watermarking techniques through a comprehensive survey of the research literature. Our work has two key advantages: (1) We analyze research based on the specific intentions behind different watermarking techniques, evaluation datasets used, and watermarking addition and removal methods to construct a cohesive taxonomy. (2) We highlight the gaps and open challenges in text watermarking to promote research protecting text authorship. This extensive coverage and detailed analysis sets our work apart, outlining the evolving landscape of text watermarking in Language Models.
RePrompt: Planning by Automatic Prompt Engineering for Large Language Models Agents
Venue: arXiv cs.CL 2025
Year: 2025

In the past year, large language models (LLMs) have had remarkable success in domains outside the traditional natural language processing, and their capacity is further expanded into the so-called LLM agents when connected with external tools. In all domains, the prompt to the LLMs has been shown to make a big difference in what the LLM would generate and thus affect the performance of the LLM agents. Therefore, automatic prompt engineering (APE) has become an important question for many researchers and users of LLMs. However, previous works in APE rely on a final checker to evaluate the performance of the given prompt -- a requirement that is hard to meet in the case of LLM agents, where intermediate feedback is easier to obtain, and the final evaluation could be expensive, inaccurate, or even missing. In this paper, we propose a novel method, \textsc{RePrompt}, which does a ``gradient descent"-like approach to optimize the step-by-step instructions in the prompts given to LLM agents, based on the chat history obtained from interactions and reflections with LLM agents. By leveraging intermediate feedback, \textsc{RePrompt} can optimize the prompt without the need for a final solution checker. We evaluate our approach on PDDL generation, TravelPlanner, and Meeting Planning to show that our method could generally improve performance for different reasoning tasks.
SilverSpeak: Evading AI-Generated Text Detectors using Homoglyphs
Venue: arXiv cs.CL 2025
Year: 2025

The advent of Large Language Models (LLMs) has enabled the generation of text that increasingly exhibits human-like characteristics. As the detection of such content is of significant importance, substantial research has been conducted with the objective of developing reliable AI-generated text detectors. These detectors have demonstrated promising results on test data, but recent research has revealed that they can be circumvented by employing different techniques. In this paper, we present homoglyph-based attacks (A $\rightarrow$ Cyrillic A) as a means of circumventing existing detectors. We conduct a comprehensive evaluation to assess the effectiveness of these attacks on seven detectors, including ArguGPT, Binoculars, DetectGPT, Fast-DetectGPT, Ghostbuster, OpenAI's detector, and watermarking techniques, on five different datasets. Our findings demonstrate that homoglyph-based attacks can effectively circumvent state-of-the-art detectors, leading them to classify all texts as either AI-generated or human-written (decreasing the average Matthews Correlation Coefficient from 0.64 to -0.01). Through further examination, we extract the technical justification underlying the success of the attacks, which varies across detectors. Finally, we discuss the implications of these findings and potential defenses against such attacks.
Deep-Reinforcement-Learning-Based AoI-Aware Resource Allocation for RIS-Aided IoV Networks
Venue: arXiv cs.LG 2025
Year: 2025

Reconfigurable Intelligent Surface (RIS) is a pivotal technology in communication, offering an alternative path that significantly enhances the link quality in wireless communication environments. In this paper, we propose a RIS-assisted internet of vehicles (IoV) network, considering the vehicle-to-everything (V2X) communication method. In addition, in order to improve the timeliness of vehicle-to-infrastructure (V2I) links and the stability of vehicle-to-vehicle (V2V) links, we introduce the age of information (AoI) model and the payload transmission probability model. Therefore, with the objective of minimizing the AoI of V2I links and prioritizing transmission of V2V links payload, we construct this optimization problem as an Markov decision process (MDP) problem in which the BS serves as an agent to allocate resources and control phase-shift for the vehicles using the soft actor-critic (SAC) algorithm, which gradually converges and maintains a high stability. A AoI-aware joint vehicular resource allocation and RIS phase-shift control scheme based on SAC algorithm is proposed and simulation results show that its convergence speed, cumulative reward, AoI performance, and payload transmission probability outperforms those of proximal policy optimization (PPO), deep deterministic policy gradient (DDPG), twin delayed deep deterministic policy gradient (TD3) and stochastic algorithms.
Embedded Hierarchical MPC for Autonomous Navigation
Venue: arXiv cs.RO 2025
Year: 2025

To efficiently deploy robotic systems in society, mobile robots must move autonomously and safely through complex environments. Nonlinear model predictive control (MPC) methods provide a natural way to find a dynamically feasible trajectory through the environment without colliding with nearby obstacles. However, the limited computation power available on typical embedded robotic systems, such as quadrotors, poses a challenge to running MPC in real time, including its most expensive tasks: constraints generation and optimization. To address this problem, we propose a novel hierarchical MPC scheme that consists of a planning and a tracking layer. The planner constructs a trajectory with a long prediction horizon at a slow rate, while the tracker ensures trajectory tracking at a relatively fast rate. We prove that the proposed framework avoids collisions and is recursively feasible. Furthermore, we demonstrate its effectiveness in simulations and lab experiments with a quadrotor that needs to reach a goal position in a complex static environment. The code is efficiently implemented on the quadrotor's embedded computer to ensure real-time feasibility. Compared to a state-of-the-art single-layer MPC formulation, this allows us to increase the planning horizon by a factor of 5, which results in significantly better performance.
Pre-Training and Personalized Fine-Tuning via Over-the-Air Federated Meta-Learning: Convergence-Generalization Trade-Offs
Venue: arXiv cs.LG 2025
Year: 2025

For modern artificial intelligence (AI) applications such as large language models (LLMs), the training paradigm has recently shifted to pre-training followed by fine-tuning. Furthermore, owing to dwindling open repositories of data and thanks to efforts to democratize access to AI models, pre-training is expected to increasingly migrate from the current centralized deployments to federated learning (FL) implementations. Meta-learning provides a general framework in which pre-training and fine-tuning can be formalized. Meta-learning-based personalized FL (meta-pFL) moves beyond basic personalization by targeting generalization to new agents and tasks. This paper studies the generalization performance of meta-pFL for a wireless setting in which the agents participating in the pre-training phase, i.e., meta-learning, are connected via a shared wireless channel to the server. Adopting over-the-air computing, we study the trade-off between generalization to new agents and tasks, on the one hand, and convergence, on the other hand. The trade-off arises from the fact that channel impairments may enhance generalization, while degrading convergence. Extensive numerical results validate the theory.
Treewidth Inapproximability and Tight ETH Lower Bound
Venue: arXiv cs.CC 2025
Year: 2025

We present a simple, self-contained, linear reduction from 3-SAT to Treewidth. Specifically, it shows that 1.00005-approximating Treewidth is NP-hard, and solving Treewidth exactly requires $2^{Ω(n)}$ time, unless the Exponential-Time Hypothesis fails. We further derive, under the latter assumption, that there are some constants $δ> 1$ and $c>0$ such that $δ$-approximating Treewidth requires time $2^{Ω(n/\log^c n)}$.
Unveiling the Power of Source: Source-based Minimum Bayes Risk Decoding for Neural Machine Translation
Venue: arXiv cs.CL 2025
Year: 2025

Maximum a posteriori decoding, a commonly used method for neural machine translation (NMT), aims to maximize the estimated posterior probability. However, high estimated probability does not always lead to high translation quality. Minimum Bayes Risk (MBR) decoding offers an alternative by seeking hypotheses with the highest expected utility. Inspired by Quality Estimation (QE) reranking which uses the QE model as a ranker we propose source-based MBR (sMBR) decoding, a novel approach that utilizes quasi-sources (generated via paraphrasing or back-translation) as ``support hypotheses'' and a reference-free quality estimation metric as the utility function, marking the first work to solely use sources in MBR decoding. Experiments show that sMBR outperforms QE reranking and the standard MBR decoding. Our findings suggest that sMBR is a promising approach for NMT decoding.
A Deep Learning Framework for Evaluating Dynamic Network Generative Models and Anomaly Detection
Venue: arXiv cs.SI 2025
Year: 2025

Understanding dynamic systems like disease outbreaks, social influence, and information diffusion requires effective modeling of complex networks. Traditional evaluation methods for static networks often fall short when applied to temporal networks. This paper introduces DGSP-GCN (Dynamic Graph Similarity Prediction based on Graph Convolutional Network), a deep learning-based framework that integrates graph convolutional networks with dynamic graph signal processing techniques to provide a unified solution for evaluating generative models and detecting anomalies in dynamic networks. DGSP-GCN assesses how well a generated network snapshot matches the expected temporal evolution, incorporating an attention mechanism to improve embedding quality and capture dynamic structural changes. The approach was tested on five real-world datasets: WikiMath, Chickenpox, PedalMe, MontevideoBus, and MetraLa. Results show that DGSP-GCN outperforms baseline methods, such as time series regression and random similarity assignment, achieving the lowest error rates (MSE of 0.0645, MAE of 0.1781, RMSE of 0.2507). These findings highlight DGSP-GCN's effectiveness in evaluating and detecting anomalies in dynamic networks, offering valuable insights for network evolution and anomaly detection research.